Remove mix-max dead code and --method CLI flag

[wsnoble]

Summary

• Removes the MixmaxConfidence class (~177 lines) from confidence.py — the mix-max method was previously removed but its class was left behind
• Removes mixmax(), estimate_pi0(), and calculate_mixmax_qval() from qvalues.py (~211 lines) — these only served mix-max
• Removes the --method/-m CLI flag from params.py — its only remaining choice was "tdc", making it a no-op
• Removes the method parameter from PsmDataset.assign_confidence() and dataset.py's internal dispatch dict, replacing method-based dispatch with a direct TdcConfidence(...) call (the backend parameter added in PR29 is preserved)
• Cleans up unused imports: itertools in utils.py, ClassVar in dataset.py, re in three parsers, read_txt/read_pepxml in msfragger.py
• Fixes test fixtures to use Path(__file__).parent.parent / "data" so tests pass regardless of the working directory from which pytest is run

Test plan

• Full test suite passes: pytest tests/ → 88 passed, 2 skipped
• All method="tdc" kwargs removed from all test files (test_confidence.py, test_edge_cases.py, test_writers.py)
• No mixmax fixtures or tests remain in test_qvalues.py or test_confidence.py
• numba import retained in qvalues.py — still used by _fdr2qvalue

🤖 Generated with Claude Code

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: fc79ac62-3844-4eb1-b694-0a6a696fbe6d

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch remove-dead-code

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}

[Copilot]

Pull request overview

This PR removes the previously-deprecated MixMax confidence/q-value implementation and simplifies the confidence estimation API/CLI to the single remaining method (TDC), while updating tests and fixtures accordingly.

Changes:

• Deleted MixMax-related code paths (MixmaxConfidence and mixmax q-value helpers) and removed method-based dispatch in PsmDataset.assign_confidence().
• Removed the no-op --method/-m CLI flag and updated CLI dispatch to match the new API.
• Updated unit tests/fixtures to remove method="tdc" usage and to use a stable DATA_DIR path independent of the current working directory.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/unit_tests/test_writers.py	Removes method="tdc" from confidence assignment calls in writer tests.
tests/unit_tests/test_qvalues.py	Removes MixMax imports and MixMax test coverage; keeps TDC tests.
tests/unit_tests/test_parquet.py	Removes method="tdc" from Parquet writer tests.
tests/unit_tests/test_edge_cases.py	Removes method="tdc" from edge-case confidence assignment tests.
tests/unit_tests/test_duckdb.py	Updates backend validation test to check unknown backend rather than invalid method.
tests/unit_tests/test_confidence.py	Removes MixMax confidence tests and method="tdc" usage; keeps TDC tests.
tests/conftest.py	Introduces DATA_DIR fixture root to make test data paths robust to pytest CWD.
crema/utils.py	Ensures parse_psms_txt doesn’t use the pyarrow engine when skiprows is required.
crema/qvalues.py	Removes MixMax q-value estimation functions, leaving TDC and helper _fdr2qvalue.
crema/params.py	Removes the --method/-m CLI argument.
crema/dataset.py	Removes method dispatch and always instantiates TdcConfidence for pandas backend; preserves backend selection.
crema/crema.py	Stops passing args.method into assign_confidence now that the flag/parameter is removed.
crema/confidence.py	Removes the MixmaxConfidence class implementation.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.